{"files"=>["https://ndownloader.figshare.com/files/1265207"], "description"=>"<p>(A) Quantitative PCR analysis was performed for ten DNA segments of the <i>Cah1</i> locus and enrichment of each fragment was measured. Red areas show the location of the DNA segments amplified and quantified. Exons are indicated by blue boxes and introns by dashed lines. (B) DNA segments located in the promoter region (amplicons B and C) and in a region located in the last exon of the <i>Cah1</i> gene, representing the 3´ UTR (amplicons I and J), were found to be enriched. De-crosslinked chromatin was used as control for calculating the enrichment of genomic fragments in the FAIRE samples. The enrichment was determined as 2<sup>-ΔΔCt</sup> (cf. Material and Methods) and error bars indicate the standard deviation (SD) from three biological replicates. The reference region H is indicated by a star (*) in (A) and refers to the region where the C<sub>t</sub> value ratio between FAIRE and control samples was the lowest. The C<sub>t</sub> values of the reference region were used for the calculation of the FAIRE enrichment as a normalization parameter. The position of regulatory elements of the LC response previously identified by Kucho et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079909#B24\" target=\"_blank\">24</a>] is indicated. </p>", "links"=>[], "tags"=>["pcr", "faire", "fragments", "derived"], "article_id"=>840307, "categories"=>["Biological Sciences"], "users"=>["Flavia Vischi Winck", "Samuel Arvidsson", "Diego Mauricio Riaño-Pachón", "Sabrina Hempel", "Aneta Koseska", "Zoran Nikoloski", "David Alejandro Urbina Gomez", "Jens Rupprecht", "Bernd Mueller-Roeber"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0079909.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_PCR_of_FAIRE_fragments_derived_from_the_Cah1_locus_/840307", "title"=>"Quantitative PCR of FAIRE fragments derived from the <i>Cah1</i> locus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:12:28"}

{"files"=>["https://ndownloader.figshare.com/files/1265211"], "description"=>"<p>Genomic coordinates were used to calculate the distances between FAIRE summits and the start and stop codons of their nearest gene transcripts. The number of transcripts with at least one FAIRE peak assigned was counted and the distances to the start or stop codons computed. The gray line indicates the cumulative percentage of the transcripts to which FAIRE peaks were assigned. As seen, approximately 80% of the FAIRE summits were located within 1.5 kb up- or downstream of the transcript´s start or stop codon. FAIRE peaks were detected using MACS tool v. 1.4.0beta, with a <i>p</i>-value cutoff equal to 10<sup>-05</sup>.</p>", "links"=>[], "tags"=>["histogram", "approximate", "distances", "faire", "summits", "annotated"], "article_id"=>840310, "categories"=>["Biological Sciences"], "users"=>["Flavia Vischi Winck", "Samuel Arvidsson", "Diego Mauricio Riaño-Pachón", "Sabrina Hempel", "Aneta Koseska", "Zoran Nikoloski", "David Alejandro Urbina Gomez", "Jens Rupprecht", "Bernd Mueller-Roeber"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0079909.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cumulative_histogram_of_the_approximate_distances_of_FAIRE_summits_from_their_next_closest_annotated_gene_/840310", "title"=>"Cumulative histogram of the approximate distances of FAIRE summits from their next closest annotated gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:12:28"}